Locus 3827

Sequence ID 3R_DroMel_CAF1
Location 10,434,412 – 10,434,562
Length 150
Max. P 0.976173
window6130 window6131

overview

Window 0

Location 10,434,412 – 10,434,525
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.22
Mean single sequence MFE -35.18
Consensus MFE -27.00
Energy contribution -29.86
Covariance contribution 2.86
Combinations/Pair 1.10
Mean z-score -2.59
Structure conservation index 0.77
SVM decision value 1.76
SVM RNA-class probability 0.976173
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10434412 113 + 27905053
GCAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCUCAUAGGAGUACUCAGUACCCAGCAU-------CCAUCCUCGUCGGGCUGCCUCCAGCAUCCGCCACUCGAGGGCAUACAU
(.(((((.......((((....))))..(((((....)......((.((((...)))))).))))-------.....((((...((((((.....)))...)))...))))))))).).. ( -33.60)
>DroSec_CAF1 97792 113 + 1
GUAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCUCAUAGGAGUACCCAAUACCCAGCAU-------CCAUCCUCGUCGGGCUGCCACCAGCAUCCGCCACUCGAGGGAAUACAU
((((..........((((....))))..(((((....)......((.(((.....))))).))))-------...((((((...((((((.....)))...)))...)))))).)))).. ( -30.00)
>DroSim_CAF1 86003 113 + 1
GUAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCUCAUAGGAGUACCCAGUACCCAGCAU-------CCAUCCUCGUCGGACUGCCACCAGCAUCCGCCACUCGAGGGCAUACAU
(((((((.......((((....))))..(((((....)......((.((((...)))))).))))-------.....((((.((((.(((.....))))))).....))))))))))).. ( -37.50)
>DroEre_CAF1 94906 113 + 1
GUAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCCCAUAGGAGUGCCCAAUACCCAGCAU-------CCAUCCUCAUUGGGCUGCCACCAGCAUCCGCCACUCGGGGGCAUACAU
(((((((........(((....)))((...(((((....(((.((((((((..........))))-------...))))...)))((((....)))).)))))...))...))))))).. ( -38.90)
>DroYak_CAF1 96368 107 + 1
GCAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCUCAUAGGAGUACCCAGUACCCAGCAUGCUGCCUGCAUCCUCUUUGGACUGC-------------CACUCGGGGGCAUGCAC
(((((((.......((((....))))..(((((....)......((.((((...)))))).))))....(((((((((.....))).)))-------------.....)))))))))).. ( -35.90)
>consensus
GUAUGCCACAAAAAUGCUGAAAAGCGAAAUGCGGAAACCUCAUAGGAGUACCCAGUACCCAGCAU_______CCAUCCUCGUCGGGCUGCCACCAGCAUCCGCCACUCGAGGGCAUACAU
(((((((.......((((....))))..(((((....)......((.(((.....))))).))))............((((...((((((.....)))...)))...))))))))))).. (-27.00 = -29.86 +   2.86)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,434,452 – 10,434,562
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.07
Mean single sequence MFE -34.74
Consensus MFE -23.20
Energy contribution -24.84
Covariance contribution 1.64
Combinations/Pair 1.11
Mean z-score -1.70
Structure conservation index 0.67
SVM decision value 0.06
SVM RNA-class probability 0.562344
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10434452 110 + 27905053
CAUAGGAGUACUCAGUACCCAGCAU-------CCAUCCUCGUCGGGCUGCCUCCAGCAUCCGCCACUCGAGGGCAUACAUGGAUCCAUAUAUGCAGUGUAGCUGAGGAACAAA---AAAG
..............((.((((((..-------....(((((...((((((.....)))...)))...)))))(((((.(((....))).)))))......)))).)).))...---.... ( -34.40)
>DroSec_CAF1 97832 112 + 1
CAUAGGAGUACCCAAUACCCAGCAU-------CCAUCCUCGUCGGGCUGCCACCAGCAUCCGCCACUCGAGGGAAUACAUGGAUCCAUAUAUGCAGUGCAGCUGAGGGACAAAA-AAAAG
....((.....))....((((((((-------(((((((((...((((((.....)))...)))...)))))......)))))).......(((...))))))).)).......-..... ( -29.90)
>DroSim_CAF1 86043 113 + 1
CAUAGGAGUACCCAGUACCCAGCAU-------CCAUCCUCGUCGGACUGCCACCAGCAUCCGCCACUCGAGGGCAUACAUGGAUCCAUAUAUGCAGUGUAGCUGAGGAACAAAAAAAAAG
....((.....)).((.((((((..-------....(((((.((((.(((.....))))))).....)))))(((((.(((....))).)))))......)))).)).)).......... ( -34.80)
>DroEre_CAF1 94946 112 + 1
CAUAGGAGUGCCCAAUACCCAGCAU-------CCAUCCUCAUUGGGCUGCCACCAGCAUCCGCCACUCGGGGGCAUACAUGGAUCCAUAUAUGCCGUGUAGCUGAGGGGCAAAA-AAAGG
........(((((........((((-------(((.......)))).)))...((((.((((.....))))((((((.(((....))).)))))).....))))..)))))...-..... ( -36.60)
>DroYak_CAF1 96408 105 + 1
CAUAGGAGUACCCAGUACCCAGCAUGCUGCCUGCAUCCUCUUUGGACUGC-------------CACUCGGGGGCAUGCACGGCUCCAUAUAUGCAGUGCAGCUUUGGGGCAAAA-AUA-G
....((.((((...)))))).(((((((.((.((((((.....))).)))-------------.....)).)))))))...((((((....(((...)))....))))))....-...-. ( -38.00)
>consensus
CAUAGGAGUACCCAGUACCCAGCAU_______CCAUCCUCGUCGGGCUGCCACCAGCAUCCGCCACUCGAGGGCAUACAUGGAUCCAUAUAUGCAGUGUAGCUGAGGGACAAAA_AAAAG
....((.....))....((((((.............(((((...((((((.....)))...)))...)))))(((((.(((....))).)))))......)))).))............. (-23.20 = -24.84 +   1.64)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:02 2006